please would you advise, based on your experience, which algorithm is more reliable in confidently calling INDELS in cancer genomes (I am referring especially to INDELS of length > 50bp, let's say 50bp-500bp long).

Thank you Kevin. I have been inspecting cgpPINDEL : https://github.com/cancerit/cgpPindel, as they provide also a docker container. Please would you let me know : is cgpPINDEL largely equivalent to PINDEL ? Thanks !